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Snowflake: visualizing microbiome abundance tables as multivariate bipartite graphs.

作者信息

Peeters Jannes, Bot Daniël M, Rovelo Ruiz Gustavo, Aerts Jan

机构信息

Data Science Institute, Hasselt University, Diepenbeek, Belgium.

Expertise Center for Digital Media, Hasselt University-Flanders Make, Diepenbeek, Belgium.

出版信息

Front Bioinform. 2024 Feb 5;4:1331043. doi: 10.3389/fbinf.2024.1331043. eCollection 2024.


DOI:10.3389/fbinf.2024.1331043
PMID:38375239
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10875061/
Abstract

Current visualizations in microbiome research rely on aggregations in taxonomic classifications or do not show less abundant taxa. We introduce Snowflake: a new visualization method that creates a clear overview of the microbiome composition in collected samples without losing any information due to classification or neglecting less abundant reads. Snowflake displays every observed OTU/ASV in the microbiome abundance table and provides a solution to include the data's hierarchical structure and additional information obtained from downstream analysis (e.g., alpha- and beta-diversity) and metadata. Based on the value-driven ICE-T evaluation methodology, Snowflake was positively received. Experts in microbiome research found the visualizations to be user-friendly and detailed and liked the possibility of including and relating additional information to the microbiome's composition. Exploring the topological structure of the microbiome abundance table allows them to quickly identify which taxa are unique to specific samples and which are shared among multiple samples (i.e., separating sample-specific taxa from the core microbiome), and see the compositional differences between samples. An R package for constructing and visualizing Snowflake microbiome composition graphs is available at https://gitlab.com/vda-lab/snowflake.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/724d/10875061/1e4e741d85e9/fbinf-04-1331043-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/724d/10875061/8a26d05c6220/fbinf-04-1331043-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/724d/10875061/2b3525104cc9/fbinf-04-1331043-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/724d/10875061/2a15364a3424/fbinf-04-1331043-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/724d/10875061/5a36dbecc235/fbinf-04-1331043-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/724d/10875061/99c46abcc8f7/fbinf-04-1331043-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/724d/10875061/3409d2da92de/fbinf-04-1331043-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/724d/10875061/1e4e741d85e9/fbinf-04-1331043-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/724d/10875061/8a26d05c6220/fbinf-04-1331043-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/724d/10875061/2b3525104cc9/fbinf-04-1331043-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/724d/10875061/2a15364a3424/fbinf-04-1331043-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/724d/10875061/5a36dbecc235/fbinf-04-1331043-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/724d/10875061/99c46abcc8f7/fbinf-04-1331043-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/724d/10875061/3409d2da92de/fbinf-04-1331043-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/724d/10875061/1e4e741d85e9/fbinf-04-1331043-g007.jpg

相似文献

[1]
Snowflake: visualizing microbiome abundance tables as multivariate bipartite graphs.

Front Bioinform. 2024-2-5

[2]
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[3]
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[6]
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[7]
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[8]
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[9]
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[10]
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本文引用的文献

[1]
Contamination detection and microbiome exploration with GRIMER.

Gigascience. 2022-12-28

[2]
Modeling the ribosome as a bipartite graph.

PLoS One. 2022

[3]
Exploring the Microbiome Analysis and Visualization Landscape.

Front Bioinform. 2021-12-2

[4]
Comparative Evaluation of Bipartite, Node-Link, and Matrix-Based Network Representations.

IEEE Trans Vis Comput Graph. 2023-1

[5]
High-Salt Diet Induces Depletion of Lactic Acid-Producing Bacteria in Murine Gut.

Nutrients. 2022-3-10

[6]
The role of the vaginal microbiome in distinguishing female chronic pelvic pain caused by endometriosis/adenomyosis.

Ann Transl Med. 2021-5

[7]
Bipartite graph-based approach for clustering of cell lines by gene expression-drug response associations.

Bioinformatics. 2021-9-9

[8]
MicrobiomeExplorer: an R package for the analysis and visualization of microbial communities.

Bioinformatics. 2021-6-9

[9]
Lactation and menstruation shift the vaginal microbiota in captive rhesus monkeys to be more similar to the male urethral microbiota.

Sci Rep. 2019-11-22

[10]
Exploring the evolutionary dynamics of Rhizobium plasmids through bipartite network analysis.

Environ Microbiol. 2019-8-16

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